RetrogeneDB ID: retro_meug_2064

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold86145:10339..10949(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PGAP2
• Ensembl ID: ENSMEUG00000009912
• Aliases: None
• Description: post-GPI attachment to proteins 2 [Source:HGNC Symbol;Acc:17893]

Sequence

>retro_meug_2064
CACTTCATGGAGACCACATCCACCCACTGTGGGGTGCCCAATTACCTTTCCAGGGGGGAGTTCAGCCATTGCTGGGGAAG
TGTCCCAGTATGTCTGGAGTTTCTGCATCGGCCTGCACTCTGTCCACTTCTTGGTGGCCTTTGTCCGCTAGAACTACTAC
AGAAACTGCCCTTCACATTGCTTTGGCTATGACCAGCTCTGCTTTCTCAGCCTCCTAGAGAATGTGGCCCTGTTTCTCCT
CATCTATGTCTCCTCCTCAGAGGACTTCACCATCTATGAGAATGCTTTCATAGTGTTCATCACAGCAGCTTTGGGCGACA
CACTGCTAAGTTGTATCTTGTCGTGTCTGACCAAGAAACATACAATAACTTTGGAGGAACATAAGTCCTACACCTGGAAA
TAATGACTTTTTATTGTCAACTTTCTCTCTTTCTTTATGGCCCTACCCGTCTACTTCTGACATATGTACTGTGAGCCAGG
AGTGTACACCATCTTTGTGGTCCTTGAGTACACTGTGGTTATGATTAACATGGCTATGCTTATGACAGCCTCTTGGGACT
TTGAGAACAAAGAGGTGTTCATTGCTCACTTGATAGAAGATAAAAGATTC

Alignment

ORF - retro_meug_2064 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.99 %
• Parental protein coverage: 67.09 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HFEYTVATDCGVPNYL-PSVSSAIGGEVPQRYVWRFCIGLHSAPRFLVAFVYWNYYRSCPSPCFGYDQLC
          HF..T..T.CGVPNYL.P..SSAI.GEV.Q.YVW.FCIGLHS...FLVAFV..NYYR.CPS.CFGYDQLC
Retrocopy HFMETTSTHCGVPNYL>PGGSSAIAGEVSQ-YVWSFCIGLHSV-HFLVAFVR*NYYRNCPSHCFGYDQLC

Parental  LLNLGLNLLENVALLLLTYVSSSEDFTIHENAFIVFIAAALGHMLLTCILWRLTKKHTVSLEERKSYSWK
          .....L.LLENVAL.LL.YVSSSEDFTI.ENAFIVFI.AALG..LL.CIL..LTKKHT..LEE.KSY.WK
Retrocopy F----LSLLENVALFLLIYVSSSEDFTIYENAFIVFITAALGDTLLSCILSCLTKKHTITLEEHKSYTWK

Parental  QRLFIVNFVSFFMALAVYFRHNMYCEPGVYTIFAVFEYTVVLTNMGFHMTACWDFGNKEVFITSPTEDKR
          ..LFIVNF.SFFMAL.VYF.H.MYCEPGVYTIF.V.EYTVV..NM...MTA.WDF.NKEVFI....EDKR
Retrocopy **LFIVNFLSFFMALPVYF*H-MYCEPGVYTIFVVLEYTVVMINMAMLMTASWDFENKEVFIAHLIEDKR

Parental  F
          F
Retrocopy F

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_2064 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_2064 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015470	1 retrocopy	retro_cjac_4056,
Macropus eugenii	ENSMEUG00000009912	1 retrocopy	retro_meug_2064 ,
Rattus norvegicus	ENSRNOG00000020371	1 retrocopy	retro_rnor_2731,